Phylotranscriptomic insights into Mesoproterozoic-Neoproterozoic origin and early radiation of green seaweeds (Ulvophyceae)

In this study, we applied coalescence- and concatenation-based approaches to reconstruct the phylogenetic relationship of Ulvophyceae through extensive nuclear gene and taxon sampling. The Ulvophyceae was robustly recovered as a paraphyletic group, in which Bryopsidales was sister to the Chlorophyceae, and the remaining Ulvophyceae was divided into three subclades. All of our analyses received mostly consistent topologies except for the branching order of the three subclades. The gene tree heterogeneity and coalescent simulation suggested that the topological conflict among these subclades could be well explained by ancient incomplete lineage sorting (ILS), and the multispecies coalescent model fits our dataset better than concatenation. Molecular clock analyses were performed with 200 clock-like genes and three calibration strategies. Our dating analyses emphasized the necessity for careful assessment of the fossil calibrations and supported that Ulvophyceae originated in the late Mesoproterozoic to early Neoproterozoic, earlier than previous studies. As photoautotrophic eukaryotes, the ulvophycean origin and early diversification may have had a profound influence on the oceanic redox structure and biochemical cycle of the earth in the Mesoproterozoic and Neoproterozoic Era.